Motion artifacts compromise the quality of magnetic resonance imaging (MRI) and pose challenges to achieving diagnostic outcomes and image-guided therapies. In recent years, supervised deep learning approaches have emerged as successful solutions for motion artifact reduction (MAR). One disadvantage of these methods is their dependency on acquiring paired sets of motion artifact-corrupted (MA-corrupted) and motion artifact-free (MA-free) MR images for training purposes. Obtaining such image pairs is difficult and therefore limits the application of supervised training. In this paper, we propose a novel UNsupervised Abnormality Extraction Network (UNAEN) to alleviate this problem. Our network is capable of working with unpaired MA-corrupted and MA-free images. It converts the MA-corrupted images to MA-reduced images by extracting abnormalities from the MA-corrupted images using a proposed artifact extractor, which intercepts the residual artifact maps from the MA-corrupted MR images explicitly, and a reconstructor to restore the original input from the MA-reduced images. The performance of UNAEN was assessed by experimenting with various publicly available MRI datasets and comparing them with state-of-the-art methods. The quantitative evaluation demonstrates the superiority of UNAEN over alternative MAR methods and visually exhibits fewer residual artifacts. Our results substantiate the potential of UNAEN as a promising solution applicable in real-world clinical environments, with the capability to enhance diagnostic accuracy and facilitate image-guided therapies.

Routine knee MRI protocols for 1.5 T and 3 T scanners, do not include T2*-w gradient echo (T2*W) images, which are useful in several clinical scenarios such as the assessment of cartilage, synovial blooming (deposition of hemosiderin), chondrocalcinosis and the evaluation of the physis in pediatric patients. Herein, we aimed to develop an open-source deep learning model that creates synthetic T2*W images of the knee using fat-suppressed intermediate-weighted images. A cycleGAN model was trained with 12,118 sagittal knee MR images and tested on an independent set of 2996 images. Diagnostic interchangeability of synthetic T2*W images was assessed against a series of findings. Voxel intensity of four tissues was evaluated with Bland-Altman plots. Image quality was assessed with the use of root mean squared error (NRMSE), structural similarity index (SSIM) and peak signal-to-noise ratio (PSNR). Code, model and a standalone executable file are provided on github. The model achieved a median NRMSE, PSNR and SSIM of 0.5, 17.4, and 0.5, respectively. Images were found interchangeable with an intraclass correlation coefficient >0.95 for all findings. Mean voxel intensity was equal between synthetic and conventional images. Four types of artifacts were identified: geometrical distortion (86/163 cases), object insertion/omission (11/163 cases), a wrap-around-like (26/163 cases) and an incomplete fat-suppression artifact (120/163 cases), which had a median 0 impact (no impact) on the diagnosis. In conclusion, the developed open-source GAN model creates synthetic T2*W images of the knee of high diagnostic value and quality. The identified artifacts had no or minor effect on the diagnostic value of the images.

Alzheimer's disease (AD) is a severe neurological illness that demolishes memory and brain functioning. This disease affects an individual's capacity to work, think, and behave. The proportion of individuals suffering from AD is rapidly increasing. It flatters a leading cause of disability and impacts millions of people worldwide. Early detection reduces disease expansion, provides more effective therapies, and leads to better results. However, predicting AD at an early stage is complex since its clinical symptoms match with normal aging, mild cognitive impairment (MCI), and neurodegenerative disorders. Prior studies indicate that early diagnosis is improved by the utilization of magnetic resonance imaging (MRI). However, MRI data is scarce, noisy, and extremely diverse among scanners and patient populations. The 2D CNNs analyze 3D data slices separately, resulting in a loss of inter-slice information and contextual coherence required to detect subtle and diffuse brain alterations. This study offered a novel 3Dimensional-Convolutional Neural Network (3D-CNN) and intelligent preprocessing pipeline for AD prediction. This work uses an intelligent frame selection and 3D dilated convolutions mechanism to recognize the most informative slices associated with AD disease. This enabled the model to capture subtle and diffuse structural changes across the brain visible in MRI scans. The proposed model examined brain structures by recognizing small volumetric changes associated with AD and acquiring spatial hierarchies within MRI data. After conducting various experiments, we observed that the proposed 3D-CNNs are highly proficient in capturing early brain changes. To validate the model's performance, a benchmark dataset called AD Neuroimaging Initiative (ADNI) is used and achieves a maximum accuracy of 92.89 %, outperforming state-of-the-art approaches.

Adolescent major depressive disorder (MDD) is a serious mental health condition that has been linked to abnormal functional connectivity (FC) patterns within the brain. However, whether FC could be used as a potential biomarker for diagnosis of adolescent MDD is still unclear. The aim of our study was to investigate the potential diagnostic value of whole-brain FC in adolescent MDD. Resting-state functional magnetic resonance imaging data were obtained from 94 adolescents with MDD and 78 healthy adolescents. The whole brain was segmented into 90 regions of interest (ROIs) using the automated anatomical labeling atlas. FC was assessed by calculating the Pearson correlation coefficient of the average time series between each pair of ROIs. A multivariate pattern analysis was employed to classify patients from controls using the whole-brain FC as input features. The linear support vector machine classifier achieved an accuracy of 69.18% using the optimal functional connection features. The consensus functional connections were mainly located within and between large-scale brain networks. The top 10 nodes with the highest weight in the classification model were mainly located in the default mode, salience, auditory, and sensorimotor networks. Our findings highlighted the importance of functional network connectivity in the neurobiology of adolescent MDD, and suggested the possibility of altered FC and high-weight regions as complementary diagnostic markers in adolescents with depression.

Diffusion models have garnered significant attention for MRI Super-Resolution (SR) and have achieved promising results. However, existing diffusion-based SR models face two formidable challenges: 1) insufficient exploitation of complementary information from multi-contrast images, which hinders the faithful reconstruction of texture details and anatomical structures; and 2) reliance on fixed magnification factors, such as 2× or 4×, which is impractical for clinical scenarios that require arbitrary scale magnification. To circumvent these issues, this paper introduces IM-Diff, an implicit multi-contrast diffusion model for arbitrary-scale MRI SR, leveraging the merits of both multi-contrast information and the continuous nature of implicit neural representation (INR). Firstly, we propose an innovative hierarchical multi-contrast fusion (HMF) module with reference-aware cross Mamba (RCM) to effectively incorporate target-relevant information from the reference image into the target image, while ensuring a substantial receptive field with computational efficiency. Secondly, we introduce multiple wavelet INR magnification (WINRM) modules into the denoising process by integrating the wavelet implicit neural non-linearity, enabling effective learning of continuous representations of MR images. The involved wavelet activation enhances space-frequency concentration, further bolstering representation accuracy and robustness in INR. Extensive experiments on three public datasets demonstrate the superiority of our method over existing state-of-the-art SR models across various magnification factors.

Schizophrenia (SCH) is a complex neurodevelopmental disorder, whose pathogenesis is not fully elucidated. This article aims to reveal disease-specific brain structural and functional changes and their potential genetic basis by analyzing the characteristics of brain magnetic resonance imaging (MRI) in SCH patients and related gene expression patterns. Differentially expressed genes (DEGs) between SCH and healthy control (NC) groups in the GSE48072 dataset were identified and functionally analyzed, and a protein-protein interaction (PPI) network was fabricated to screen for core genes (CGs). Meanwhile, MRI data from the COBRE, the Human Connectome Project (HCP), the 1000 Functional Connectomes Project (FCP), and the Consortium for Reliability and Reproducibility (CoRR) were utilized to explore differences in brain activity patterns between SCH patients and NC group using a 3D deep aggregation network (3D DANet) machine learning approach. A correlation analysis was performed between the identified CGs and MRI imaging characteristics. 82 DEGs were collected from the GSE48072 dataset, primarily involved in cytotoxic granules, growth factor binding, and graft-versus-host disease pathways. The construction of the PPI network revealed KLRD1, KLRF1, CD244, GZMH, GZMA, GZMB, PRF1, and SLAMF6 as CGs. SCH patients exhibited relatively enhanced activity patterns in the frontoparietal attention network (FAN) and default mode network (DMN) across four datasets, while showing a trend of weakening in most other networks. The 3D DANet demonstrated higher accuracy, specificity, and sensitivity in brain image classification. The correlation between enhancement of the DMN and genetic abnormalities was the strongest, followed by the enhancement of the frontal and parietal attention networks. In contrast, the correlation between the weakening of the sensory-motor network and occipital network and genetic abnormalities was relatively weak. The strongest correlation was observed between MRI characteristics and the KLRD1 and CD244 genes. The granzyme-mediated programmed cell death signaling pathway is related to pathogenesis of SCH, and CD244 may serve as potential biological markers for diagnosing SCH. The correlation between enhancement of the DMN and genetic abnormalities was the strongest, followed by the enhancement of the frontal and parietal attention networks. In contrast, the correlation between weakening of the sensory-motor network and occipital network and genetic abnormalities was relatively weak. Additionally, the strongest correlation was observed between MRI features and the KLRD1 and CD244 genes. The use of the 3D DANet method has improved the detection precision of brain structural and functional changes in SCH patients, providing a new perspective for understanding the biological basis of the disease.

Deep learning frameworks utilizing convolutional neural networks (CNNs) have frequently been used for brain age prediction and have achieved outstanding performance. Nevertheless, deep learning remains a black box as it is hard to interpret which brain parts contribute significantly to the predictions. To tackle this challenge, we first trained a lightweight, fully CNN model for brain age estimation on a large sample data set (N = 3054, age range = [8,80 years]) and tested it on an independent data set (N = 555, age range = [8,80 years]). We then developed an interpretable scheme combining network occlusion sensitivity analysis (NOSA) with a fine-grained human brain atlas to uncover the learned invariance of the model. Our findings show that the dorsolateral, dorsomedial frontal cortex, anterior cingulate cortex, and thalamus had the highest contributions to age prediction across the lifespan. More interestingly, we observed that different regions showed divergent patterns in their predictions for specific age groups and that the bilateral hemispheres contributed differently to the predictions. Regions in the frontal lobe were essential predictors in both the developmental and aging stages, with the thalamus remaining relatively stable and saliently correlated with other regional changes throughout the lifespan. The lateral and medial temporal brain regions gradually became involved during the aging phase. At the network level, the frontoparietal and the default mode networks show an inverted U-shape contribution from the developmental to the aging stages. The framework could identify regional contributions to the brain age prediction model, which could help increase the model interpretability when serving as an aging biomarker.

There is an urgent need for the precise prediction of cerebral amyloidosis using noninvasive and accessible indicators to facilitate the early diagnosis of individuals with the preclinical stage of Alzheimer's disease (AD). Two hundred and four individuals with subjective cognitive decline (SCD) were enrolled in this study. All subjects completed neuropsychological assessments and underwent 18F-florbetapir PET, structural MRI, and functional MRI. A total of 315 features were extracted from the MRI, demographics, and neuropsychological scales and selected using the least absolute shrinkage and selection operator (LASSO). The logistic regression (LR) model, based on machine learning, was trained to classify SCD as either β-amyloid (Aβ) positive or negative. A nomogram was established using a multivariate LR model to predict the risk of Aβ+. The performance of the prediction model and nomogram was assessed with area under the curve (AUC) and calibration. The final model was based on the right rostral anterior cingulate thickness, the grey matter volume of the right inferior temporal, the ReHo of the left posterior cingulate gyrus and right superior temporal gyrus, as well as MoCA-B and AVLT-R. In the training set, the model achieved a good AUC of 0.78 for predicting Aβ+, with an accuracy of 0.72. The validation of the model also yielded a favorable discriminatory ability with an AUC of 0.88 and an accuracy of 0.83. We have established and validated a model based on cognitive, sMRI, and fMRI data that exhibits adequate discrimination. This model has the potential to predict amyloid status in the SCD group and provide a noninvasive, cost-effective way that might facilitate early screening, clinical diagnosis, and drug clinical trials.

Brain disorder diagnosis via resting-state functional magnetic resonance imaging (rs-fMRI) is usually limited due to the complex imaging features and sample size. For brain disorder diagnosis, the graph convolutional network (GCN) has achieved remarkable success by capturing interactions between individuals and the population. However, there are mainly three limitations: 1) The previous GCN approaches consider the non-imaging information in edge construction but ignore the sensitivity differences of features to non-imaging information. 2) The previous GCN approaches solely focus on establishing interactions between subjects (i.e., individuals and the population), disregarding the essential relationship between features. 3) Multisite data increase the sample size to help classifier training, but the inter-site heterogeneity limits the performance to some extent. This paper proposes a knowledge-aware multisite adaptive graph Transformer to address the above problems. First, we evaluate the sensitivity of features to each piece of non-imaging information, and then construct feature-sensitive and feature-insensitive subgraphs. Second, after fusing the above subgraphs, we integrate a Transformer module to capture the intrinsic relationship between features. Third, we design a domain adaptive GCN using multiple loss function terms to relieve data heterogeneity and to produce the final classification results. Last, the proposed framework is validated on two brain disorder diagnostic tasks. Experimental results show that the proposed framework can achieve state-of-the-art performance.